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This best-selling volume presents the principles and applications of physical chemistry as they are used to solve problems in biology and medicine.The First Law; the Second Law; free energy and chemical equilibria; free energy and physical Equilibria; molecular motion and transport properties; kinetics: rates of chemical reactions; enzyme kinetics; the theory and spectroscopy of molecular structures and interactions: molecular distributions and statistical thermodynamics; and macromolecular structure and X-ray diffraction.For anyone interested in physical chemistry as it relates to problems in biology and medicine.

Ignacio Tinoco was an undergraduate at the University of New Mexico, a graduate student at the University of Wisconsin, and a postdoctoral fellow at Yale. He then went to the University of California, Berkeley, where he has remained. His research interest has been on the structures of nucleic acids, particularly RNA. He was chairman of the Department of Energy committee that recommended in 1987 a major initiative to sequence the human genome. His present research is on unfolding single RNA molecules by force.

Kenneth Sauer grew up in Cleveland, Ohio, and received his A.B. in chemistry from Oberlin College. Following his Ph.D. studies in gas-phase physical chemistry at Harvard, he spent three years teaching at the American University of Beirut, Lebanon. A postdoctoral opportunity to learn from Melvin Calvin about photosynthesis in plants led him to the University of California, Berkeley, where he has been since 1960. Teaching general chemistry and biophysical chemistry in the Chemistry Department has complemented research in the Physical Biosciences Division of the Lawrence Berkeley National Lab involving spectroscopic studies of photosynthetic light reactions and their role in water oxidation. His other activities include reading, renaissance and baroque choral music, canoeing, and exploring the Sierra Nevada with his family and friends.

James C. Wang was on the faculty of the University of California, Berkeley, from 1966 to 1977. He then joined the faculty of Harvard University, where he is presently Mallinckrodt Professor of Biochemistry and Molecular Biology. His research focuses on DNA and enzymes that act on DNA, especially a class of enzymes known as DNA topoisomerases. He has taught courses in biophysical chemistry and molecular biology and has published over 200 research articles. He is a member of Academia Sinica, the American Academy of Arts and Sciences, and the U.S. National Academy of Sciences.

Joseph Puglisi was born and raised in New Jersey. He received his B.A. in chemistry from The Johns Hopkins University in 1984 and his Ph.D. from the University of California, Berkeley, in 1989. He has studied and taught in Strasbourg, Boston, and Santa Cruz, and is currently professor of structural biology at Stanford University. His research interests are in the structure and mechanism of the ribosome and the use of NMR spectroscopy to study RNA structure. He has been a Dreyfus Scholar, Sloan Scholar, and Packard Fellow.

Preface

xvii

About the Authors

xix

Introduction

The Human Genome and Beyond

4

(2)

Transcription and Translation

6

(4)

Ion Channels

10

(1)

References

11

(1)

Suggested Reading

12

(1)

Problem

12

(3)

The First Law: Energy Is Conserved

Concepts

15

(1)

Applications

16

(1)

Energy Conversion and Conservation

16

(13)

Systems and Surroundings

17

(1)

Energy Exchanges

18

(10)

First Law of Thermodynamics

28

(1)

Describing the State of a System

29

(16)

Variables of State

29

(2)

Equations of State

31

(2)

Paths Connecting Different States

33

(3)

Dependence of the Energy and Enthalpy of a Pure Substance on P, V, and T

36

(8)

Relations Between Heat Exchanges and DE and DH

44

(1)

Phase Changes

45

(2)

Chemical Reactions

47

(9)

Heat Effects of Chemical Reactions

47

(3)

Temperature Dependence of ΔH

50

(1)

The Energy Change ΔE for a Reaction

51

(1)

Standard Enthalpies (or Heats) of Formation

51

(2)

Bond Energies

53

(3)

Molecular Interpretations of Energy and Enthalpy

56

(1)

Summary

57

(3)

State Variables

57

(1)

Unit Conversions

57

(1)

General Equations

57

(1)

Pressure-Volume Work Only

58

(1)

Solids and Liquids

58

(1)

Gases

59

(1)

Phase Changes

59

(1)

Chemical Reactions

60

(1)

Mathematics Needed for Chapter 2

60

(1)

References

61

(1)

Suggested Reading

61

(1)

Problems

61

(8)

The Second Law: The Entropy of the Universe Increases

Concepts

69

(1)

Applications

69

(1)

Historical Development of the Second Law: The Carnot Cycle

69

(4)

A New State Function, Entropy

73

(2)

The Second Law of Thermodynamics: Entropy Is Not Conserved

75

(2)

Molecular Interpretation of Entropy

77

(4)

Fluctuations

79

(2)

Measurement of Entropy

81

(1)

Chemical Reactions

81

(1)

Third Law of Thermodynamics

82

(5)

Temperature Dependence of Entropy

82

(1)

Temperature Dependence of the Entropy Change for a Chemical Reaction

83

(1)

Entropy Change for a Phase Transition

84

(1)

Pressure Dependence of Entropy

85

(2)

Spontaneous Chemical Reactions

87

(1)

Gibbs Free Energy

87

(10)

ΔG and a System's Capacity to Do Nonexpansion Work

87

(1)

Spontaneous Reactions at Constant T and P

88

(1)

Calculation of Gibbs Free Energy

89

(2)

Temperature Dependence of Gibbs Free Energy

91

(3)

Pressure Dependence of Gibbs Free Energy

94

(3)

Phase Changes

97

(1)

Helmholtz Free Energy

97

(1)

Noncovalent Reactions

97

(9)

Hydrophobic Interactions

100

(1)

Proteins and Nucleic Acids

101

(5)

Use of Partial Derivatives in Thermodynamics

106

(5)

Relations Among Partial Derivatives

107

(4)

Summary

111

(2)

State Variables

111

(1)

Unit Conversions

111

(1)

General Equations

111

(1)

ΔG and a System's Capacity to Do Nonexpansion Work

111

(1)

Spontaneous Reactions at Constant T and P

111

(1)

Changes in Entropy and Gibbs Free Energy

112

(1)

References

113

(1)

Suggested Reading

113

(1)

Problems

113

(8)

Free Energy and Chemical Equilibria

Concepts

121

(1)

Applications

122

(1)

Chemical Potential (Partial Molar Gibbs Free Energy)

122

(3)

Gibbs Free Energy and the Chemical Potential

122

(1)

The Sum Rule for Partial Molar Quantities

123

(1)

Chemical Potential and Directionality of Chemical Reaction

123

(2)

Reactions of Gases: The Ideal Gas Approximation

125

(5)

Dependence of Chemical Potential on Partial Pressures

125

(2)

Equilibrium Constant

127

(3)

Nonideal Systems

130

(11)

Activity

130

(1)

Standard States

131

(8)

Activity Coefficients of Ions

139

(2)

The Equilibrium Constant and the Standard Gibbs Free Energies of the Reactants and Products

141

(12)

Calculation of Equilibrium Concentrations: Ideal Solutions

144

(6)

Temperature Dependence of the Equilibrium Constant

150

(3)

Galvanic Cells

153

(6)

Standard Electrode Potentials

156

(2)

Concentration Dependence of

158

(1)

Biochemical Applications of Thermodynamics

159

(11)

Thermodynamics of Metabolism

165

(5)

Biological Redox Reactions

170

(6)

NADH-Q Reductase

171

(1)

Cytochrome Reductase

172

(1)

Cytochrome c Oxidase

172

(1)

Double Strand Formation in Nucleic Acids

172

(3)

Ionic Effect on Protein-Nucleic Acid Interactions

175

(1)

Summary

176

(3)

Chemical Potential (Partial Molar Gibbs Free Energy)

176

(1)

Standard States and Activities

177

(1)

Gibbs Free-Energy Change and Equilibrium Constant for a Chemical Reaction

Calculation of Diffracted Intensities from Atomic Coordinates: The Structure Factor

684

(2)

Calculation of Atomic Coordinates from Diffracted Intensities

686

(2)

The Phase Problem

688

(1)

Direct Methods

688

(1)

Isomorphous Replacement

688

(2)

Multiwavelength Anomalous Diffraction

690

(1)

Determination of a Crystal Structure

691

(3)

Scattering of X Rays by Noncrystalline Materials

694

(1)

Absorption of X Rays

695

(1)

Extended Fine Structure of Edge Absorption

696

(1)

X Rays from Synchrotron Radiation

697

(1)

Electron Diffraction

698

(1)

Neutron Diffraction

699

(1)

Electron Microscopy

700

(4)

Resolution, Contrast, and Radiation Damage

700

(1)

Transmission and Scanning Electron Microscopes

701

(1)

Image Enhancement and Reconstruction

701

(1)

Scanning Tunneling and Atomic Force Microscopy

702

(2)

Summary

704

(3)

X-ray Diffraction

704

(3)

Neutron Diffraction

707

(1)

Electron Microscopy

707

(1)

Mathematics Needed for Chapter 12

707

(1)

References

708

(1)

Suggested Reading

708

(1)

Problems

709

(3)

Appendix

712

(13)

Answers

725

(3)

Index

728

PREFACE There is a deep sense of pleasure to be experienced when the patterns and symmetry of nature are revealed. Physical chemistry provides the methods to discover and understand these patterns. We think that not only is it important to learn and apply physical chemistry to biological problems, it may even be fun. In this book, we have tried to capture some of the excitement of making new discoveries and finding answers to fundamental questions. This is not an encyclopedia of physical chemistry. Rather, we have written this text specifically with the life-science student in mind. We present a streamlined treatment that covers the core aspects of biophysical chemistry (thermodynamics and kinetics as well as quantum mechanics, spectroscopy, and X-ray diffraction), which are of great importance to students of biology and biochemistry. Essentially all applications of the concepts are to systems of interest to life-science students; nearly all the problems apply to life-science examples. For this fourth edition we are joined by Joseph Puglisi, a new, young author who strengthens the structural biology content of the book. We have also tried to make the book more reader-friendly. In particular, we omit fewer steps in the explanations to make the material more understandable, and we have followed the many helpful and specific recommendations of our reviewers to improve the writing throughout. Important new topics, such as single-molecule thermodynamics, kinetics, and spectroscopy, are introduced. Subjects that have become less pertinent to current biophysical chemistry have been deleted or de-emphasized. Reference lists for each chapter have been updated. However, the format and organization of the book is essentially unchanged. Chapter 1 introduces representative areas of active current research in biophysical chemistry and molecular biology: the human genome, the transfer of genetic information from DNA to RNA to protein, ion channels, and cell-to-cell communication. We encourage students to read the current literature to see how the vocabulary and concepts of physical chemistry are used in solving biological problems. Chapters 2 through 5 cover the laws of thermodynamics and their applications to chemical reactions and physical processes. Essentially all of the examples and problems deal with biochemical and biological systems. For example, after defining work as a force multiplied by the distance moved (the displacement), we discuss the experimental measurement of the work necessary to stretch a single DNA molecule from its random-coiled form to an extended rod. Molecular interpretations of energies and entropies are emphasized in each of the chapters. Chapter 4, "Free Energy and Chemical Equilibria," now starts with the application of the chemical potential td chemical reactions. We think that this will make it easier to understand the logic relating activities and equilibrium constants to free energy. Binding of ligands and equilibria between phases are described in chapter 5, "Free Energy and Physical Equilibria." We discuss in detail the allosteric effect and the cooperative binding of oxygen by hemoglobin. We also describe the formation of lipid monolayers, lipid bilayers, and micelles, and their structures are compared to biological membranes. Chapters 6 through 8 cover molecular motion and chemical kinetics. Chapter 6, "Molecular Motion and Transport Properties," starts with the Brownian motion on an aqueous surface of a single lipid molecule labeled with a fluorescent dye. The random motion of the molecule can be followed to test Einstein's equation relating average distance traveled by a single molecule to a bulk diffusion coefficient. Following this direct experimental demonstration of thermal motion of a molecule, we introduce the kinetic theory of gases and discuss transport properties (diffusion, sedimentation, and electrophoresis) of macromolecules. The next two chap